Microarray analysis has begun to provide unprecedented quantities of data on patterns of gene expression on a genomic scale. The rapid refinement of laboratory protocols and the proliferation of high quality instrumentation for array printing and scanning have made microarray technology accessible to an increasing number of smaller laboratories, allowing them to investigate problems in biology using functional genomics approaches. While the technical barriers have been lowered, many labs find themselves ill equipped to deal with the vast quantities of data that typical microarray experiments, involving assays for thousands of genes across tens or hundreds of conditions, provide. In support of a number of ongoing microarray projects at TIGR, our group has developed an integrated system of software and databases for microarray data collection and analysis. The goal of this proposed project is to provide an integrated, extensible system for microarray data management and analysis free of charge to the research community using an open-source philosophy for distribution of source code and future community development. Following refinement and release of our present system, we will continue to improve and maintain the code, incorporating additions made at TIGR and elsewhere and providing users with regular, stable updates.